1
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Suh YJ, Li AT, Pandey M, Nordmann CS, Huang YL, Wu M. Decoding physical principles of cell migration under controlled environment using microfluidics. BIOPHYSICS REVIEWS 2024; 5:031302. [PMID: 39091432 PMCID: PMC11290890 DOI: 10.1063/5.0199161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/26/2024] [Indexed: 08/04/2024]
Abstract
Living cells can perform incredible tasks that man-made micro/nano-sized robots have not yet been able to accomplish. One example is that white blood cells can sense and move to the site of pathogen attack within minutes. The robustness and precision of cellular functions have been perfected through billions of years of evolution. In this context, we ask the question whether cells follow a set of physical principles to sense, adapt, and migrate. Microfluidics has emerged as an enabling technology for recreating well-defined cellular environment for cell migration studies, and its ability to follow single cell dynamics allows for the results to be amenable for theoretical modeling. In this review, we focus on the development of microfluidic platforms for recreating cellular biophysical (e.g., mechanical stress) and biochemical (e.g., nutrients and cytokines) environments for cell migration studies in 3D. We summarize the basic principles that cells (including bacteria, algal, and mammalian cells) use to respond to chemical gradients learned from microfluidic systems. We also discuss about novel biological insights gained from studies of cell migration under biophysical cues and the need for further quantitative studies of cell function under well-controlled biophysical environments in the future.
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Affiliation(s)
- Young Joon Suh
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Alan T. Li
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Mrinal Pandey
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Cassidy S. Nordmann
- Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Yu Ling Huang
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, New York 14853, USA
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2
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Liu F, Deroy C, Herr AE. Microfluidics for macrofluidics: addressing marine-ecosystem challenges in an era of climate change. LAB ON A CHIP 2024. [PMID: 39093009 DOI: 10.1039/d4lc00468j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Climate change presents a mounting challenge with profound impacts on ocean and marine ecosystems, leading to significant environmental, health, and economic consequences. Microfluidic technologies, with their unique capabilities, play a crucial role in understanding and addressing the marine aspects of the climate crisis. These technologies leverage quantitative, precise, and miniaturized formats that enhance the capabilities of sensing, imaging, and molecular tools. Such advancements are critical for monitoring marine systems under the stress of climate change and elucidating their response mechanisms. This review explores microfluidic technologies employed both in laboratory settings for testing and in the field for monitoring purposes. We delve into the application of miniaturized tools in evaluating ocean-based solutions to climate change, thus offering fresh perspectives from the solution-oriented end of the spectrum. We further aim to synthesize recent developments in technology around critical questions concerning the ocean environment and marine ecosystems, while discussing the potential for future innovations in microfluidic technology. The purpose of this review is to enhance understanding of current capabilities and assist researchers interested in mitigating the effects of climate change to identify new avenues for tackling the pressing issues posed by climate change in marine ecosystems.
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Affiliation(s)
- Fangchen Liu
- Department of Bioengineering, University of California, Berkeley, California 94158, USA.
| | - Cyril Deroy
- Department of Bioengineering, University of California, Berkeley, California 94158, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California 94158, USA.
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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3
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Moore JP, Kamino K, Kottou R, Shimizu TS, Emonet T. Signal integration and adaptive sensory diversity tuning in Escherichia coli chemotaxis. Cell Syst 2024; 15:628-638.e8. [PMID: 38981486 PMCID: PMC11307269 DOI: 10.1016/j.cels.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/01/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of E. coli integrate multiple chemical signals to adjust sensory diversity in response to changes in the prevalence of each ligand in the environment. Measuring kinase activity in single cells, we quantified the sensitivity distribution to various chemoattractants in different mixtures of background stimuli. We found that when ligands bind uncompetitively, the population tunes sensory diversity to each signal independently, decreasing diversity when the signal's ambient concentration increases. However, among competitive ligands, the population can only decrease sensory diversity one ligand at a time. Mathematical modeling suggests that sensory diversity tuning benefits E. coli populations by modulating how many cells are committed to tracking each signal proportionally as their prevalence changes.
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Affiliation(s)
- Jeremy Philippe Moore
- Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | - Keita Kamino
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Rafaela Kottou
- Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | | | - Thierry Emonet
- Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA; Department of Physics, Yale University, New Haven, CT 06511, USA.
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4
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Moore JP, Kamino K, Kottou R, Shimizu TS, Emonet T. Signal Integration and Adaptive Sensory Diversity Tuning in Escherichia coli Chemotaxis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.08.527720. [PMID: 36798398 PMCID: PMC9934624 DOI: 10.1101/2023.02.08.527720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
In uncertain environments, phenotypic diversity can be advantageous for survival. However, as the environmental uncertainty decreases, the relative advantage of having diverse phenotypes decreases. Here, we show how populations of E. coli integrate multiple chemical signals to adjust sensory diversity in response to changes in the prevalence of each ligand in the environment. Measuring kinase activity in single cells, we quantified the sensitivity distribution to various chemoattractants in different mixtures of background stimuli. We found that when ligands bind uncompetitively, the population tunes sensory diversity to each signal independently, decreasing diversity when the signal ambient concentration increases. However, amongst competitive ligands the population can only decrease sensory diversity one ligand at a time. Mathematical modeling suggests that sensory diversity tuning benefits E. coli populations by modulating how many cells are committed to tracking each signal proportionally as their prevalence changes.
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5
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Baverstock K. Responses to commentaries on "The gene: An appraisal". PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 188:31-42. [PMID: 38360273 DOI: 10.1016/j.pbiomolbio.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/02/2024] [Indexed: 02/17/2024]
Abstract
The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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7
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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8
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. Proc Natl Acad Sci U S A 2024; 121:e2309251121. [PMID: 38194458 PMCID: PMC10801886 DOI: 10.1073/pnas.2309251121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
| | - Jonathan S. Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
| | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA20147
- HHMI, University of California, San Diego, CA92093
- Department of Neurosciences, University of California, San Diego, CA92093
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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9
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Baverstock K. The Gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:e73-e88. [PMID: 38044248 DOI: 10.1016/j.pbiomolbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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10
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Huang S, Wu J, Zheng L, Long Y, Chen J, Li J, Dai B, Lin F, Zhuang S, Zhang D. 3D free-assembly modular microfluidics inspired by movable type printing. MICROSYSTEMS & NANOENGINEERING 2023; 9:111. [PMID: 37705925 PMCID: PMC10495351 DOI: 10.1038/s41378-023-00585-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 09/15/2023]
Abstract
Reconfigurable modular microfluidics presents an opportunity for flexibly constructing prototypes of advanced microfluidic systems. Nevertheless, the strategy of directly integrating modules cannot easily fulfill the requirements of common applications, e.g., the incorporation of materials with biochemical compatibility and optical transparency and the execution of small batch production of disposable chips for laboratory trials and initial tests. Here, we propose a manufacturing scheme inspired by the movable type printing technique to realize 3D free-assembly modular microfluidics. Double-layer 3D microfluidic structures can be produced by replicating the assembled molds. A library of modularized molds is presented for flow control, droplet generation and manipulation and cell trapping and coculture. In addition, a variety of modularized attachments, including valves, light sources and microscopic cameras, have been developed with the capability to be mounted onto chips on demand. Microfluidic systems, including those for concentration gradient generation, droplet-based microfluidics, cell trapping and drug screening, are demonstrated. This scheme enables rapid prototyping of microfluidic systems and construction of on-chip research platforms, with the intent of achieving high efficiency of proof-of-concept tests and small batch manufacturing.
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Affiliation(s)
- Shaoqi Huang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Jiandong Wu
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Lulu Zheng
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Yan Long
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Junyi Chen
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Jianlang Li
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Bo Dai
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Francis Lin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Songlin Zhuang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
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11
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Zamani-Dahaj SA, Burnetti A, Day TC, Yunker PJ, Ratcliff WC, Herron MD. Spontaneous Emergence of Multicellular Heritability. Genes (Basel) 2023; 14:1635. [PMID: 37628687 PMCID: PMC10454505 DOI: 10.3390/genes14081635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The major transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. Using analytical models, synthetic biology, and biologically-informed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Prior work on the evolution of multicellularity has asserted that substantial collective-level trait heritability either emerges only late in the transition or requires some evolutionary change subsequent to the formation of clonal multicellular groups. In a prior analytical model, we showed that collective-level heritability not only exists but is usually more heritable than the underlying cell-level trait upon which it is based, as soon as multicellular groups form. Here, we show that key assumptions and predictions of that model are borne out in a real engineered biological system, with important implications for the emergence of collective-level heritability.
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Affiliation(s)
- Seyed Alireza Zamani-Dahaj
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - Anthony Burnetti
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
| | - Thomas C. Day
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - Peter J. Yunker
- Georgia Institute of Technology, School of Physics, Atlanta, GA 30332, USA; (T.C.D.); (P.J.Y.)
| | - William C. Ratcliff
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
| | - Matthew D. Herron
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA 30332, USA; (A.B.); (M.D.H.)
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12
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Phan TV, Mattingly HH, Vo L, Marvin JS, Looger LL, Emonet T. Direct measurement of dynamic attractant gradients reveals breakdown of the Patlak-Keller-Segel chemotaxis model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543315. [PMID: 37333331 PMCID: PMC10274659 DOI: 10.1101/2023.06.01.543315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Chemotactic bacteria not only navigate chemical gradients, but also shape their environments by consuming and secreting attractants. Investigating how these processes influence the dynamics of bacterial populations has been challenging because of a lack of experimental methods for measuring spatial profiles of chemoattractants in real time. Here, we use a fluorescent sensor for aspartate to directly measure bacterially generated chemoattractant gradients during collective migration. Our measurements show that the standard Patlak-Keller-Segel model for collective chemotactic bacterial migration breaks down at high cell densities. To address this, we propose modifications to the model that consider the impact of cell density on bacterial chemotaxis and attractant consumption. With these changes, the model explains our experimental data across all cell densities, offering new insight into chemotactic dynamics. Our findings highlight the significance of considering cell density effects on bacterial behavior, and the potential for fluorescent metabolite sensors to shed light on the complex emergent dynamics of bacterial communities.
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Affiliation(s)
- Trung V. Phan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Lam Vo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
| | | | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
- Howard Hughes Medical Institute, Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT
- Quantitative Biology Institute, Yale University, New Haven, CT
- Department of Physics, Yale University, New Haven, CT
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13
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Ma ZC, Fan J, Wang H, Chen W, Yang GZ, Han B. Microfluidic Approaches for Microactuators: From Fabrication, Actuation, to Functionalization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300469. [PMID: 36855777 DOI: 10.1002/smll.202300469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Indexed: 06/02/2023]
Abstract
Microactuators can autonomously convert external energy into specific mechanical motions. With the feature sizes varying from the micrometer to millimeter scale, microactuators offer many operation and control possibilities for miniaturized devices. In recent years, advanced microfluidic techniques have revolutionized the fabrication, actuation, and functionalization of microactuators. Microfluidics can not only facilitate fabrication with continuously changing materials but also deliver various signals to stimulate the microactuators as desired, and consequently improve microfluidic chips with multiple functions. Herein, this cross-field that systematically correlates microactuator properties and microfluidic functions is comprehensively reviewed. The fabrication strategies are classified into two types according to the flow state of the microfluids: stop-flow and continuous-flow prototyping. The working mechanism of microactuators in microfluidic chips is discussed in detail. Finally, the applications of microactuator-enriched functional chips, which include tunable imaging devices, micromanipulation tools, micromotors, and microsensors, are summarized. The existing challenges and future perspectives are also discussed. It is believed that with the rapid progress of this cutting-edge field, intelligent microsystems may realize high-throughput manipulation, characterization, and analysis of tiny objects and find broad applications in various fields, such as tissue engineering, micro/nanorobotics, and analytical devices.
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Affiliation(s)
- Zhuo-Chen Ma
- Department of Automation, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Shanghai Engineering Research Center of Intelligent Control and Management, Shanghai, 200240, China
- Institute of Medical Robotics, School of Biomedical Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiahao Fan
- Department of Automation, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Shanghai Engineering Research Center of Intelligent Control and Management, Shanghai, 200240, China
| | - Hesheng Wang
- Department of Automation, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Shanghai Engineering Research Center of Intelligent Control and Management, Shanghai, 200240, China
| | - Weidong Chen
- Department of Automation, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
- Shanghai Engineering Research Center of Intelligent Control and Management, Shanghai, 200240, China
- Institute of Medical Robotics, School of Biomedical Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Guang-Zhong Yang
- Institute of Medical Robotics, School of Biomedical Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
| | - Bing Han
- Institute of Medical Robotics, School of Biomedical Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
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14
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Dutta S. Most probable paths for active Ornstein-Uhlenbeck particles. Phys Rev E 2023; 107:054130. [PMID: 37329007 DOI: 10.1103/physreve.107.054130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 05/05/2023] [Indexed: 06/18/2023]
Abstract
Fluctuations play an important role in the dynamics of stochastic systems. In particular, for small systems, the most probable thermodynamic quantities differ from their averages because of the fluctuations. Using the Onsager Machlup variational formalism we analyze the most probable paths for nonequilibrium systems, in particular, active Ornstein-Uhlenbeck particles, and investigate how the entropy production along these paths differs from the average entropy production. We investigate how much information about their nonequilibrium nature can be obtained from their extremum paths and how these paths depend on the persistence time and their swim velocities. We also look at how the entropy production along the most probable paths varies with the active noise and how it differs from the average entropy production. This study would be useful to design artificial active systems with certain target trajectories.
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Affiliation(s)
- Sandipan Dutta
- Department of Physics, Birla Institute of Technology and Science, Pilani, Rajasthan, 333031, India
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15
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Gotovtsev P. Microbial Cells as a Microrobots: From Drug Delivery to Advanced Biosensors. Biomimetics (Basel) 2023; 8:biomimetics8010109. [PMID: 36975339 PMCID: PMC10046805 DOI: 10.3390/biomimetics8010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The presented review focused on the microbial cell based system. This approach is based on the application of microorganisms as the main part of a robot that is responsible for the motility, cargo shipping, and in some cases, the production of useful chemicals. Living cells in such microrobots have both advantages and disadvantages. Regarding the advantages, it is necessary to mention the motility of cells, which can be natural chemotaxis or phototaxis, depending on the organism. There are approaches to make cells magnetotactic by adding nanoparticles to their surface. Today, the results of the development of such microrobots have been widely discussed. It has been shown that there is a possibility of combining different types of taxis to enhance the control level of the microrobots based on the microorganisms' cells and the efficiency of the solving task. Another advantage is the possibility of applying the whole potential of synthetic biology to make the behavior of the cells more controllable and complex. Biosynthesis of the cargo, advanced sensing, on/off switches, and other promising approaches are discussed within the context of the application for the microrobots. Thus, a synthetic biology application offers significant perspectives on microbial cell based microrobot development. Disadvantages that follow from the nature of microbial cells such as the number of external factors influence the cells, potential immune reaction, etc. They provide several limitations in the application, but do not decrease the bright perspectives of microrobots based on the cells of the microorganisms.
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Affiliation(s)
- Pavel Gotovtsev
- National Research Center "Kurchatov Institute", Biotechnology and Bioenergy Department, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141701 Moscow, Russia
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16
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Yasuda K, Ishimoto K. Most probable path of an active Brownian particle. Phys Rev E 2022; 106:064120. [PMID: 36671105 DOI: 10.1103/physreve.106.064120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/30/2022] [Indexed: 12/23/2022]
Abstract
In this study, we investigate the transition path of a free active Brownian particle (ABP) on a two-dimensional plane between two given states. The extremum conditions for the most probable path connecting the two states are derived using the Onsager-Machlup integral and its variational principle. We provide explicit solutions to these extremum conditions and demonstrate their nonuniqueness through an analogy with the pendulum equation indicating possible multiple paths. The pendulum analogy is also employed to characterize the shape of the globally most probable path obtained by explicitly calculating the path probability for multiple solutions. We comprehensively examine a translation process of an ABP to the front as a prototypical example. Interestingly, the numerical and theoretical analyses reveal that the shape of the most probable path changes from an I to a U shape and to the ℓ shape with an increase in the transition process time. The Langevin simulation also confirms this shape transition. We also discuss further method applications for evaluating a transition path in rare events in active matter.
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Affiliation(s)
- Kento Yasuda
- Research Institute for Mathematical Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Kenta Ishimoto
- Research Institute for Mathematical Sciences, Kyoto University, Kyoto 606-8502, Japan
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17
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Macfarlane FR, Lorenzi T, Painter KJ. The Impact of Phenotypic Heterogeneity on Chemotactic Self-Organisation. Bull Math Biol 2022; 84:143. [PMID: 36319913 PMCID: PMC9626439 DOI: 10.1007/s11538-022-01099-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
The capacity to aggregate through chemosensitive movement forms a paradigm of self-organisation, with examples spanning cellular and animal systems. A basic mechanism assumes a phenotypically homogeneous population that secretes its own attractant, with the well known system introduced more than five decades ago by Keller and Segel proving resolutely popular in modelling studies. The typical assumption of population phenotypic homogeneity, however, often lies at odds with the heterogeneity of natural systems, where populations may comprise distinct phenotypes that vary according to their chemotactic ability, attractant secretion, etc. To initiate an understanding into how this diversity can impact on autoaggregation, we propose a simple extension to the classical Keller and Segel model, in which the population is divided into two distinct phenotypes: those performing chemotaxis and those producing attractant. Using a combination of linear stability analysis and numerical simulations, we demonstrate that switching between these phenotypic states alters the capacity of a population to self-aggregate. Further, we show that switching based on the local environment (population density or chemoattractant level) leads to diverse patterning and provides a route through which a population can effectively curb the size and density of an aggregate. We discuss the results in the context of real world examples of chemotactic aggregation, as well as theoretical aspects of the model such as global existence and blow-up of solutions.
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Affiliation(s)
- Fiona R Macfarlane
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Scotland.
| | - Tommaso Lorenzi
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Turin, Italy
| | - Kevin J Painter
- Inter-university Department of Regional and Urban Studies and Planning, Politecnico di Torino, Turin, Italy
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18
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Muljadi M, Fu YC, Cheng CM. Understanding the Cell's Response to Chemical Signals: Utilisation of Microfluidic Technology in Studies of Cellular and Dictyostelium discoideum Chemotaxis. MICROMACHINES 2022; 13:1737. [PMID: 36296089 PMCID: PMC9611482 DOI: 10.3390/mi13101737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Cellular chemotaxis has been the subject of a variety of studies due to its relevance in physiological processes, disease pathogenesis, and systems biology, among others. The migration of cells towards a chemical source remains a closely studied topic, with the Boyden chamber being one of the earlier techniques that has successfully studied cell chemotaxis. Despite its success, diffusion chambers such as these presented a number of problems, such as the quantification of many aspects of cell behaviour, the reproducibility of procedures, and measurement accuracy. The advent of microfluidic technology prompted more advanced studies of cell chemotaxis, usually involving the social amoeba Dictyostelium discoideum (D. discoideum) as a model organism because of its tendency to aggregate towards chemotactic agents and its similarities to higher eukaryotes. Microfluidic technology has made it possible for studies to look at chemotactic properties that would have been difficult to observe using classic diffusion chambers. Its flexibility and its ability to generate consistent concentration gradients remain some of its defining aspects, which will surely lead to an even better understanding of cell migratory behaviour and therefore many of its related biological processes. This paper first dives into a brief introduction of D. discoideum as a social organism and classical chemotaxis studies. It then moves to discuss early microfluidic devices, before diving into more recent and advanced microfluidic devices and their use with D. discoideum. The paper then closes with brief opinions about research progress in the field and where it will possibly lead in the future.
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Affiliation(s)
- Michael Muljadi
- International Intercollegiate Ph.D. Program, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yi-Chen Fu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
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19
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Hu P, Ly KL, Pham LPH, Pottash AE, Sheridan K, Wu HC, Tsao CY, Quan D, Bentley WE, Rubloff GW, Sintim HO, Luo X. Bacterial chemotaxis in static gradients quantified in a biopolymer membrane-integrated microfluidic platform. LAB ON A CHIP 2022; 22:3203-3216. [PMID: 35856590 PMCID: PMC9756273 DOI: 10.1039/d2lc00481j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemotaxis is a fundamental bacterial response mechanism to changes in chemical gradients of specific molecules known as chemoattractant or chemorepellent. The advancement of biological platforms for bacterial chemotaxis research is of significant interest for a wide range of biological and environmental studies. Many microfluidic devices have been developed for its study, but challenges still remain that can obscure analysis. For example, cell migration can be compromised by flow-induced shear stress, and bacterial motility can be impaired by nonspecific cell adhesion to microchannels. Also, devices can be complicated, expensive, and hard to assemble. We address these issues with a three-channel microfluidic platform integrated with natural biopolymer membranes that are assembled in situ. This provides several unique attributes. First, a static, steady and robust chemoattractant gradient was generated and maintained. Second, because the assembly incorporates assembly pillars, the assembled membrane arrays connecting nearby pillars can be created longer than the viewing window, enabling a wide 2D area for study. Third, the in situ assembled biopolymer membranes minimize pressure and/or chemiosmotic gradients that could induce flow and obscure chemotaxis study. Finally, nonspecific cell adhesion is avoided by priming the polydimethylsiloxane (PDMS) microchannel surfaces with Pluronic F-127. We demonstrated chemotactic migration of Escherichia coli as well as Pseudomonas aeruginosa under well-controlled easy-to-assemble glucose gradients. We characterized motility using the chemotaxis partition coefficient (CPC) and chemotaxis migration coefficient (CMC) and found our results consistent with other reports. Further, random walk trajectories of individual cells in simple bright field images were conveniently tracked and presented in rose plots. Velocities were calculated, again in agreement with previous literature. We believe the biopolymer membrane-integrated platform represents a facile and convenient system for robust quantitative assessment of cellular motility in response to various chemical cues.
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Affiliation(s)
- Piao Hu
- Department of Mechanical Engineering, Catholic University of America, Washington, District of Columbia 20064, USA.
| | - Khanh L Ly
- Department of Biomedical Engineering, Catholic University of America, Washington, District of Columbia 20064, USA
| | - Le P H Pham
- Department of Mechanical Engineering, Catholic University of America, Washington, District of Columbia 20064, USA.
| | - Alex E Pottash
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Kathleen Sheridan
- Department of Biomedical Engineering, Catholic University of America, Washington, District of Columbia 20064, USA
| | - Hsuan-Chen Wu
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Chen-Yu Tsao
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - David Quan
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
| | - Gary W Rubloff
- Department of Materials Science & Engineering, University of Maryland, College Park, MD 20742, USA
| | - Herman O Sintim
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaolong Luo
- Department of Mechanical Engineering, Catholic University of America, Washington, District of Columbia 20064, USA.
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20
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Karin O, Alon U. The dopamine circuit as a reward-taxis navigation system. PLoS Comput Biol 2022; 18:e1010340. [PMID: 35877694 PMCID: PMC9352198 DOI: 10.1371/journal.pcbi.1010340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/04/2022] [Accepted: 06/29/2022] [Indexed: 01/29/2023] Open
Abstract
Studying the brain circuits that control behavior is challenging, since in addition to their structural complexity there are continuous feedback interactions between actions and sensed inputs from the environment. It is therefore important to identify mathematical principles that can be used to develop testable hypotheses. In this study, we use ideas and concepts from systems biology to study the dopamine system, which controls learning, motivation, and movement. Using data from neuronal recordings in behavioral experiments, we developed a mathematical model for dopamine responses and the effect of dopamine on movement. We show that the dopamine system shares core functional analogies with bacterial chemotaxis. Just as chemotaxis robustly climbs chemical attractant gradients, the dopamine circuit performs ‘reward-taxis’ where the attractant is the expected value of reward. The reward-taxis mechanism provides a simple explanation for scale-invariant dopaminergic responses and for matching in free operant settings, and makes testable quantitative predictions. We propose that reward-taxis is a simple and robust navigation strategy that complements other, more goal-directed navigation mechanisms.
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Affiliation(s)
- Omer Karin
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel
- Dept. of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (OK); (UA)
| | - Uri Alon
- Dept. of Molecular Cell Biology, Weizmann Institute of Science, Rehovot Israel
- * E-mail: (OK); (UA)
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21
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Keegstra JM, Carrara F, Stocker R. The ecological roles of bacterial chemotaxis. Nat Rev Microbiol 2022; 20:491-504. [PMID: 35292761 DOI: 10.1038/s41579-022-00709-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
How bacterial chemotaxis is performed is much better understood than why. Traditionally, chemotaxis has been understood as a foraging strategy by which bacteria enhance their uptake of nutrients and energy, yet it has remained puzzling why certain less nutritious compounds are strong chemoattractants and vice versa. Recently, we have gained increased understanding of alternative ecological roles of chemotaxis, such as navigational guidance in colony expansion, localization of hosts or symbiotic partners and contribution to microbial diversity by the generation of spatial segregation in bacterial communities. Although bacterial chemotaxis has been observed in a wide range of environmental settings, insights into the phenomenon are mostly based on laboratory studies of model organisms. In this Review, we highlight how observing individual and collective migratory behaviour of bacteria in different settings informs the quantification of trade-offs, including between chemotaxis and growth. We argue that systematically mapping when and where bacteria are motile, in particular by transgenerational bacterial tracking in dynamic environments and in situ approaches from guts to oceans, will open the door to understanding the rich interplay between metabolism and growth and the contribution of chemotaxis to microbial life.
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Affiliation(s)
| | - Francesco Carrara
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland.
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22
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Shim S. Diffusiophoresis, Diffusioosmosis, and Microfluidics: Surface-Flow-Driven Phenomena in the Presence of Flow. Chem Rev 2022; 122:6986-7009. [PMID: 35285634 DOI: 10.1021/acs.chemrev.1c00571] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Diffusiophoresis is the spontaneous motion of particles under a concentration gradient of solutes. Since the first recognition by Derjaguin and colleagues in 1947 in the form of capillary osmosis, the phenomenon has been broadly investigated theoretically and experimentally. Early studies were mostly theoretical and were largely interested in surface coating applications, which considered the directional transport of coating particles. In the past decade, advances in microfluidics enabled controlled demonstrations of diffusiophoresis of micro- and nanoparticles. The electrokinetic nature and the typical scales of interest of the phenomenon motivated various experimental studies using simple microfluidic configurations. In this review, I will discuss studies that report diffusiophoresis in microfluidic systems, with the focus on the fundamental aspects of the reported results. In particular, parameters and influences of diffusiophoresis and diffusioosmosis in microfluidic systems and their combinations are highlighted.
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Affiliation(s)
- Suin Shim
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, United States
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23
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Chu HCW, Garoff S, Tilton RD, Khair AS. Tuning chemotactic and diffusiophoretic spreading via hydrodynamic flows. SOFT MATTER 2022; 18:1896-1910. [PMID: 35188176 DOI: 10.1039/d2sm00139j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The transport of microorganisms by chemotaxis is described by the same "log-sensing" response as colloids undergoing diffusiophoresis, despite their different mechanistic origins. We employ a recently-developed macrotransport theory to analyze the advective-diffusive transport of a chemotactic or diffusiophoretic colloidal species (both referred to as "colloids") in a circular tube under a steady pressure-driven flow (referred to as hydrodynamic flow) and transient solute gradient. First, we derive an exact solution to the log-sensing chemotactic/diffusiophoretic macrotransport equation. We demonstrate that a strong hydrodynamic flow can reduce spreading of solute-repelled colloids, by eliminating super-diffusion which occurs in an otherwise quiescent system. In contrast, hydrodynamic flows always enhance spreading of solute-attracted colloids. Second, we generalize the exact solution to show that the above tunable spreading phenomena by hydrodynamic flows persist quantitatively for decaying colloids, as may occur with cell death, for example. Third, we examine the spreading of chemotactic colloids by employing a more general model that captures a hallmark of chemotaxis, that log-sensing occurs only over a finite range of solute concentration. Apart from demonstrating for the first time the generality of the macrotransport theory to incorporate an arbitrary chemotactic flow model, we reveal via numerical solutions new regimes of anomalous spreading, which match qualitatively with experiments and are tunable by hydrodynamic flows. The results presented here could be employed to tailor chemotactic/diffusiophoretic colloid transport using hydrodynamic flows, which are central to applications such as oil recovery and bioremediation of aquifers.
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Affiliation(s)
- Henry C W Chu
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA.
| | - Stephen Garoff
- Department of Physics and Center for Complex Fluids Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Robert D Tilton
- Department of Chemical Engineering, Department of Biomedical Engineering and Center for Complex Fluids Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Aditya S Khair
- Department of Chemical Engineering and Center for Complex Fluids Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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24
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Computing within bacteria: Programming of bacterial behavior by means of a plasmid encoding a perceptron neural network. Biosystems 2022; 213:104608. [DOI: 10.1016/j.biosystems.2022.104608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/07/2021] [Accepted: 01/11/2022] [Indexed: 01/12/2023]
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25
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Kerk YJ, Jameel A, Xing X, Zhang C. Recent advances of integrated microfluidic suspension cell culture system. ENGINEERING BIOLOGY 2021; 5:103-119. [PMID: 36970555 PMCID: PMC9996741 DOI: 10.1049/enb2.12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.
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Affiliation(s)
- Yi Jing Kerk
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Aysha Jameel
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Xin‐Hui Xing
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| | - Chong Zhang
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
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26
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Narla AV, Cremer J, Hwa T. A traveling-wave solution for bacterial chemotaxis with growth. Proc Natl Acad Sci U S A 2021; 118:e2105138118. [PMID: 34819366 PMCID: PMC8640786 DOI: 10.1073/pnas.2105138118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
Bacterial cells navigate their environment by directing their movement along chemical gradients. This process, known as chemotaxis, can promote the rapid expansion of bacterial populations into previously unoccupied territories. However, despite numerous experimental and theoretical studies on this classical topic, chemotaxis-driven population expansion is not understood in quantitative terms. Building on recent experimental progress, we here present a detailed analytical study that provides a quantitative understanding of how chemotaxis and cell growth lead to rapid and stable expansion of bacterial populations. We provide analytical relations that accurately describe the dependence of the expansion speed and density profile of the expanding population on important molecular, cellular, and environmental parameters. In particular, expansion speeds can be boosted by orders of magnitude when the environmental availability of chemicals relative to the cellular limits of chemical sensing is high. Analytical understanding of such complex spatiotemporal dynamic processes is rare. Our analytical results and the methods employed to attain them provide a mathematical framework for investigations of the roles of taxis in diverse ecological contexts across broad parameter regimes.
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Affiliation(s)
- Avaneesh V Narla
- Department of Physics, University of California San Diego, La Jolla, CA 92093
| | - Jonas Cremer
- Biology Department, Stanford University, Stanford, CA 94305
| | - Terence Hwa
- Department of Physics, University of California San Diego, La Jolla, CA 92093;
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27
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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28
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Liu Y, Lehnert T, Gijs MAM. Effect of inoculum size and antibiotics on bacterial traveling bands in a thin microchannel defined by optical adhesive. MICROSYSTEMS & NANOENGINEERING 2021; 7:86. [PMID: 34745645 PMCID: PMC8536744 DOI: 10.1038/s41378-021-00309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Phenotypic diversity in bacterial flagella-induced motility leads to complex collective swimming patterns, appearing as traveling bands with transient locally enhanced cell densities. Traveling bands are known to be a bacterial chemotactic response to self-generated nutrient gradients during growth in resource-limited microenvironments. In this work, we studied different parameters of Escherichia coli (E. coli) collective migration, in particular the quantity of bacteria introduced initially in a microfluidic chip (inoculum size) and their exposure to antibiotics (ampicillin, ciprofloxacin, and gentamicin). We developed a hybrid polymer-glass chip with an intermediate optical adhesive layer featuring the microfluidic channel, enabling high-content imaging of the migration dynamics in a single bacterial layer, i.e., bacteria are confined in a quasi-2D space that is fully observable with a high-magnification microscope objective. On-chip bacterial motility and traveling band analysis was performed based on individual bacterial trajectories by means of custom-developed algorithms. Quantifications of swimming speed, tumble bias and effective diffusion properties allowed the assessment of phenotypic heterogeneity, resulting in variations in transient cell density distributions and swimming performance. We found that incubation of isogeneic E. coli with different inoculum sizes eventually generated different swimming phenotype distributions. Interestingly, incubation with antimicrobials promoted bacterial chemotaxis in specific cases, despite growth inhibition. Moreover, E. coli filamentation in the presence of antibiotics was assessed, and the impact on motility was evaluated. We propose that the observation of traveling bands can be explored as an alternative for fast antimicrobial susceptibility testing.
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Affiliation(s)
- Yang Liu
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Baverstock K. The gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:46-62. [PMID: 33979646 DOI: 10.1016/j.pbiomolbio.2021.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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30
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A Novel Microfluidic Device for the Neutrophil Functional Phenotype Analysis: Effects of Glucose and Its Derivatives AGEs. MICROMACHINES 2021; 12:mi12080944. [PMID: 34442566 PMCID: PMC8399494 DOI: 10.3390/mi12080944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/17/2022]
Abstract
Neutrophil dysfunction is closely related to the pathophysiology of patients with diabetes mellitus, but existing immunoassays are difficult to implement in clinical applications, and neutrophil’s chemotaxis as a functional biomarker for diabetes mellitus prognostic remains largely unexplored. Herein, a novel microfluidic device consisted of four independent test units with four cell docking structures was developed to study the neutrophil chemotaxis, which allowed multiple cell migration observations under a single field of view (FOV) and guaranteed more reliable results. In vitro studies, the chemotaxis of healthy neutrophils to N-Formyl-Met-Leu-Phe (fMLP) gradient (0, 10, 100, and 1000 nM) was concentration-dependent. The distinct promotion or suppression in the chemotaxis of metformin or pravastatin pretreated cells were observed after exposure to 100 nM fMLP gradient, indicating the feasibility and efficiency of this novel microfluidic device for clinically relevant evaluation of neutrophil functional phenotype. Further, the chemotaxis of neutrophils pretreated with 25, 50, or 70 mM of glucose was quantitatively lower than that of the control groups (i.e., 5 mM normal serum level). Neutrophils exposed to highly concentrated advanced glycation end products (AGEs) (0.2, 0.5, or 1.0 μM; 0.13 μM normal serum AGEs level), a product of prolonged hyperglycemia, showed that the higher the AGEs concentration was, the weaker the migration speed became. Specifically, neutrophils exposed to high concentrations of glucose or AGEs also showed a stronger drifting along with the flow, further demonstrating the change of neutrophil chemotaxis. Interestingly, adding the N-benzyl-4-chloro-N-cyclohexylbenzamide (FPS-ZM1) (i.e., high-affinity RAGE inhibitor) into the migration medium with AGEs could hinder the binding between AGEs and AGE receptor (RAGE) located on the neutrophil, thereby keeping the normal chemotaxis of neutrophils than the ones incubated with AGEs alone. These results revealed the negative effects of high concentrations of glucose and AGEs on the neutrophil chemotaxis, suggesting that patients with diabetes should manage serum AGEs and also pay attention to blood glucose indexes. Overall, this novel microfluidic device could significantly characterize the chemotaxis of neutrophils and have the potential to be further improved into a tool for risk stratification of diabetes mellitus.
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31
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Karin O, Alon U. Temporal fluctuations in chemotaxis gain implement a simulated-tempering strategy for efficient navigation in complex environments. iScience 2021; 24:102796. [PMID: 34345809 PMCID: PMC8319753 DOI: 10.1016/j.isci.2021.102796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/29/2021] [Accepted: 06/24/2021] [Indexed: 12/01/2022] Open
Abstract
Bacterial chemotaxis is a major testing ground for systems biology, including the role of fluctuations and individual variation. Individual bacteria vary in their tumbling frequency and adaptation time. Recently, large cell-cell variation was also discovered in chemotaxis gain, which determines the sensitivity of the tumbling rate to attractant gradients. Variation in gain is puzzling, because low gain impairs chemotactic velocity. Here, we provide a functional explanation for gain variation by establishing a formal analogy between chemotaxis and algorithms for sampling probability distributions. We show that temporal fluctuations in gain implement simulated tempering, which allows sampling of attractant distributions with many local peaks. Periods of high gain allow bacteria to detect and climb gradients quickly, and periods of low gain allow them to move to new peaks. Gain fluctuations thus allow bacteria to thrive in complex environments, and more generally they may play an important functional role for organism navigation.
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Affiliation(s)
- Omer Karin
- Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Wellcome Trust–Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Uri Alon
- Department Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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32
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Moore JP, Kamino K, Emonet T. Non-Genetic Diversity in Chemosensing and Chemotactic Behavior. Int J Mol Sci 2021; 22:6960. [PMID: 34203411 PMCID: PMC8268644 DOI: 10.3390/ijms22136960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Non-genetic phenotypic diversity plays a significant role in the chemotactic behavior of bacteria, influencing how populations sense and respond to chemical stimuli. First, we review the molecular mechanisms that generate phenotypic diversity in bacterial chemotaxis. Next, we discuss the functional consequences of phenotypic diversity for the chemosensing and chemotactic performance of single cells and populations. Finally, we discuss mechanisms that modulate the amount of phenotypic diversity in chemosensory parameters in response to changes in the environment.
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Affiliation(s)
- Jeremy Philippe Moore
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | - Keita Kamino
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
| | - Thierry Emonet
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; (J.P.M.); (K.K.)
- Quantitative Biology Institute, Yale University, New Haven, CT 06511, USA
- Department of Physics, Yale University, New Haven, CT 06511, USA
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33
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Khan A, Smith NM, Tullier MP, Roberts BS, Englert D, Pojman JA, Melvin AT. Development of a Flow-free Gradient Generator Using a Self-Adhesive Thiol-acrylate Microfluidic Resin/Hydrogel (TAMR/H) Hybrid System. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26735-26747. [PMID: 34081856 PMCID: PMC8289190 DOI: 10.1021/acsami.1c04771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Microfluidic gradient generators have been used to study cellular migration, growth, and drug response in numerous biological systems. One type of device combines a hydrogel and polydimethylsiloxane (PDMS) to generate "flow-free" gradients; however, their requirements for either negative flow or external clamps to maintain fluid-tight seals between the two layers have restricted their utility among broader applications. In this work, a two-layer, flow-free microfluidic gradient generator was developed using thiol-ene chemistry. Both rigid thiol-acrylate microfluidic resin (TAMR) and diffusive thiol-acrylate hydrogel (H) layers were synthesized from commercially available monomers at room temperature and pressure using a base-catalyzed Michael addition. The device consisted of three parallel microfluidic channels negatively imprinted in TAMR layered on top of the thiol-acrylate hydrogel to facilitate orthogonal diffusion of chemicals to the direction of flow. Upon contact, these two layers formed fluid-tight channels without any external pressure due to a strong adhesive interaction between the two layers. The diffusion of molecules through the TAMR/H system was confirmed both experimentally (using fluorescent microscopy) and computationally (using COMSOL). The performance of the TAMR/H system was compared to a conventional PDMS/agarose device with a similar geometry by studying the chemorepulsive response of a motile strain of GFP-expressing Escherichia coli. Population-based analysis confirmed a similar migratory response of both wild-type and mutant E. coli in both of the microfluidic devices. This confirmed that the TAMR/H hybrid system is a viable alternative to traditional PDMS-based microfluidic gradient generators and can be used for several different applications.
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Affiliation(s)
- Anowar
H. Khan
- Department
of Chemistry, Louisiana State University, Baton Rouge 70803, Louisiana, United States
| | - Noah Mulherin Smith
- Cain
Department of Chemical Engineering, Louisiana
State University, Baton Rouge 70803, Louisiana, United States
| | - Michael P. Tullier
- Department
of Chemistry, Louisiana State University, Baton Rouge 70803, Louisiana, United States
| | - B. Seth Roberts
- Cain
Department of Chemical Engineering, Louisiana
State University, Baton Rouge 70803, Louisiana, United States
| | - Derek Englert
- Chemical
and Materials Engineering, University of
Kentucky, Paducah 42002, Kentucky, United States
| | - John A. Pojman
- Department
of Chemistry, Louisiana State University, Baton Rouge 70803, Louisiana, United States
| | - Adam T. Melvin
- Cain
Department of Chemical Engineering, Louisiana
State University, Baton Rouge 70803, Louisiana, United States
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34
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Gurung JP, Navvab Kashani M, Agarwal S, Peralta G, Gel M, Baker MAB. Separation and enrichment of sodium-motile bacteria using cost-effective microfluidics. BIOMICROFLUIDICS 2021; 15:034108. [PMID: 34084258 PMCID: PMC8163512 DOI: 10.1063/5.0046941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/10/2021] [Indexed: 06/12/2023]
Abstract
Many motile bacteria are propelled by the rotation of flagellar filaments. This rotation is driven by a membrane protein known as the stator-complex, which drives the rotor of the bacterial flagellar motor. Torque generation is powered in most cases by proton transit through membrane protein complexes known as stators, with the next most common ionic power source being sodium. Sodium-powered stators can be studied through the use of synthetic chimeric stators that combine parts of sodium- and proton-powered stator proteins. The most well studied example is the use of the sodium-powered PomA-PotB chimeric stator unit in the naturally proton-powered Escherichia coli. Here we designed a fluidics system at low cost for rapid prototyping to separate motile and non-motile populations of bacteria while varying the ionic composition of the media and thus the sodium-motive force available to drive this chimeric flagellar motor. We measured separation efficiencies at varying ionic concentrations and confirmed using fluorescence that our device delivered eightfold enrichment of the motile proportion of a mixed population. Furthermore, our results showed that we could select bacteria from reservoirs where sodium was not initially present. Overall, this technique can be used to implement the selection of highly motile fractions from mixed liquid cultures, with applications in directed evolution to investigate the adaptation of motility in bacterial ecosystems.
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Affiliation(s)
- Jyoti P. Gurung
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Sanaz Agarwal
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Gonzalo Peralta
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, NSW 2052, Australia
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35
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Ly KL, Hu P, Pham LHP, Luo X. Flow-assembled chitosan membranes in microfluidics: recent advances and applications. J Mater Chem B 2021; 9:3258-3283. [PMID: 33725061 PMCID: PMC8369861 DOI: 10.1039/d1tb00045d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The integration of membranes in microfluidic devices has been extensively exploited for various chemical engineering and bioengineering applications over the past few decades. To augment the applicability of membrane-integrated microfluidic platforms for biomedical and tissue engineering studies, a biologically friendly fabrication process with naturally occurring materials is highly desired. The in situ preparation of membranes involving interfacial reactions between parallel laminar flows in microfluidic networks, known as the flow-assembly technique, is one of the most biocompatible approaches. Membranes of many types with flexible geometries have been successfully assembled inside complex microchannels using this facile and versatile flow-assembly approach. Chitosan is a naturally abundant polysaccharide known for its pronounced biocompatibility, biodegradability, good mechanical stability, ease of modification and processing, and film-forming ability under near-physiological conditions. Chitosan membranes assembled by flows in microfluidics are freestanding, robust, semipermeable, and well-aligned in microstructure, and show high affinity to bioactive reagents and biological components (e.g. biomolecules, nanoparticles, or cells) that provide facile biological functionalization of microdevices. Here, we discuss the recent developments and optimizations in the flow-assembly of chitosan membranes and chitosan-based membranes in microfluidics. Furthermore, we recapitulate the applications of the chitosan membrane-integrated microfluidic platforms dedicated to biology, biochemistry, and drug release fields, and envision the future developments of this important platform with versatile functions.
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Affiliation(s)
- Khanh L Ly
- Department of Biomedical Engineering, The Catholic University of America, Washington, DC 20064, USA
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36
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Yuan S, Jiang B, Peng T, Li Q, Zhou M. An Investigation of Flow Patterns and Mixing Characteristics in a Cross-Shaped Micromixer within the Laminar Regime. MICROMACHINES 2021; 12:462. [PMID: 33923993 PMCID: PMC8072938 DOI: 10.3390/mi12040462] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
A fast mixing is critical for subsequent practical development of microfluidic devices, which are often used for assays in the detection of reagents and samples. The present work sets up computational fluid dynamics simulations to explore the flow characteristic and mixing mechanism of fluids in cross-shaped mixers within the laminar regime. First, the effects of increasing an operating parameter on local mixing quality along the microchannels are investigated. It is found that sufficient diffusion cannot occur even though the concentration gradient is large at a high Reynolds number. Meanwhile, a method for calculating local mixing efficiency is also characterized. The mixing efficiency varies exponentially with the flow distance. Second, in order to optimize the cross-shaped mixer, the effects of design parameters, namely aspect ratio, mixing angle and blockage, on mixing quality are captured and the visualization of velocity and concentration distribution are demonstrated. The results show that the aspect ratio and the blockage play an important role in accelerating the mixing process. They can improve the mixing efficiency by increasing the mass transfer area and enhancing the chaotic advection, respectively. In contrast, the inflow angle that affects dispersion length is not an effective parameter. Besides, the surface roughness, which makes the disturbance of fluid flow by roughness more obvious, is considered. Three types of rough elements bring benefits for enhancing mixing quality due to the convection induced by the lateral velocity.
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Affiliation(s)
- Shuai Yuan
- College of Mechanical and Electrical Engineering, Central South University, Changsha 410083, China; (S.Y.); (B.J.); (T.P.); (Q.L.)
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China
| | - Bingyan Jiang
- College of Mechanical and Electrical Engineering, Central South University, Changsha 410083, China; (S.Y.); (B.J.); (T.P.); (Q.L.)
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China
| | - Tao Peng
- College of Mechanical and Electrical Engineering, Central South University, Changsha 410083, China; (S.Y.); (B.J.); (T.P.); (Q.L.)
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China
| | - Qiang Li
- College of Mechanical and Electrical Engineering, Central South University, Changsha 410083, China; (S.Y.); (B.J.); (T.P.); (Q.L.)
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China
| | - Mingyong Zhou
- College of Mechanical and Electrical Engineering, Central South University, Changsha 410083, China; (S.Y.); (B.J.); (T.P.); (Q.L.)
- State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083, China
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Molinaro C, Da Cunha V, Gorlas A, Iv F, Gallais L, Catchpole R, Forterre P, Baffou G. Are bacteria claustrophobic? The problem of micrometric spatial confinement for the culturing of micro-organisms. RSC Adv 2021; 11:12500-12506. [PMID: 35423787 PMCID: PMC8697133 DOI: 10.1039/d1ra00184a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
Culturing cells confined in microscale geometries has been reported in many studies this last decade, in particular following the development of microfluidic-based applications and lab-on-a-chip devices. Such studies usually examine growth of Escherichia coli. In this article, we show that E. coli may be a poor model and that spatial confinement can severely prevent the growth of many micro-organisms. By studying different bacteria and confinement geometries, we determine that the growth inhibition observed for some bacteria results from fast dioxygen depletion, inherent to spatial confinement, and not to any depletion of nutriments. This article unravels the physical origin of confinement problems in cell culture, highlighting the importance of oxygen depletion, and paves the way for the effective culturing of bacteria in confined geometries by demonstrating enhanced cell growth in confined geometries in the proximity of air bubbles.
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Affiliation(s)
- Céline Molinaro
- Institut Fresnel, CNRS, Aix Marseille University, Centrale Marseille Marseille France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Aurore Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - François Iv
- Institut Fresnel, CNRS, Aix Marseille University, Centrale Marseille Marseille France
| | - Laurent Gallais
- Institut Fresnel, CNRS, Aix Marseille University, Centrale Marseille Marseille France
| | - Ryan Catchpole
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Patrick Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC) 91198 Gif-sur-Yvette France
| | - Guillaume Baffou
- Institut Fresnel, CNRS, Aix Marseille University, Centrale Marseille Marseille France
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38
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Ruby E. Getting to know our microbial friends by dropping into their neighbourhood. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:27-30. [PMID: 33047473 DOI: 10.1111/1758-2229.12895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Edward Ruby
- Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
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39
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Mony C, Vandenkoornhuyse P, Bohannan BJM, Peay K, Leibold MA. A Landscape of Opportunities for Microbial Ecology Research. Front Microbiol 2020; 11:561427. [PMID: 33329422 PMCID: PMC7718007 DOI: 10.3389/fmicb.2020.561427] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/30/2020] [Indexed: 11/13/2022] Open
Abstract
Microbes encompass tremendous biodiversity, provide support to all living forms, including humans, and play an important role in many ecosystem services. The rules that govern microorganism community assembly are increasingly revealed due to key advances in molecular and analytical methods but their understanding remain a key challenge in microbial ecology. The existence of biogeographic patterns within microbial communities has been established and explained in relation to landscape-scale processes, including selection, drift, dispersal and mutation. The effect of habitat patchiness on microorganisms' assembly rules remains though incompletely understood. Here, we review how landscape ecology principles can be adapted to explore new perspectives on the mechanisms that determine microbial community structure. To provide a general overview, we characterize microbial landscapes, the spatial and temporal scales of the mechanisms that drive microbial assembly and the feedback between microorganisms and landscape structure. We provide evidence for the effects of landscape heterogeneity, landscape fragmentation and landscape dynamics on microbial community structure, and show that predictions made for macro-organisms at least partly also apply to microorganisms. We explain why emerging metacommunity approaches in microbial ecology should include explicit characterization of landscape structure in their development and interpretation. We also explain how biotic interactions, such as competition, prey-predator or mutualist relations may influence the microbial landscape and may be involved in the above-mentioned feedback process. However, we argue that the application of landscape ecology to the microbial world cannot simply involve transposing existing theoretical frameworks. This is due to the particularity of these organisms, in terms of size, generation time, and for some of them, tight interaction with hosts. These characteristics imply dealing with unusual and dependent space and time scales of effect. Evolutionary processes have also a strong importance in microorganisms' response to their landscapes. Lastly, microorganisms' activity and distribution induce feedback effects on the landscape that have to be taken into account. The transposition of the landscape ecology framework to microorganisms provides many challenging research directions for microbial ecology.
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Affiliation(s)
- Cendrine Mony
- UMR CNRS ECOBIO, Université de Rennes, Rennes, France
| | | | | | - Kabir Peay
- Department of Biology, University of Stanford, Stanford, CA, United States
| | - Mathew A Leibold
- Department of Biology, University of Florida, Gainesville, FL, United States
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40
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Cao M, Goodrich-Blair H. Xenorhabdus nematophila bacteria shift from mutualistic to virulent Lrp-dependent phenotypes within the receptacles of Steinernema carpocapsae insect-infective stage nematodes. Environ Microbiol 2020; 22:5433-5449. [PMID: 33078552 DOI: 10.1111/1462-2920.15286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/03/2020] [Accepted: 10/18/2020] [Indexed: 01/06/2023]
Abstract
Xenorhabdus nematophila bacteria are mutualists of Steinernema carpocapsae nematodes and pathogens of insects. Xenorhabdus nematophila exhibits phenotypic variation between insect virulence (V) and the mutualistic (M) support of nematode reproduction and colonization initiation in the infective juvenile (IJ) stage nematode that carries X. nematophila between insect hosts. The V and M phenotypes occur reciprocally depending on levels of the transcription factor Lrp: high-Lrp expressors are M+V- while low-Lrp expressors are V+M-. We report here that variable (wild type) or fixed high-Lrp expressors also are optimized, relative to low- or no-Lrp expressors, for colonization of additional nematode stages: juvenile, adult and pre-transmission infective juvenile (IJ). In contrast, we found that after the bacterial population had undergone outgrowth in mature IJs, the advantage for colonization shifted to low-Lrp expressors: fixed low-Lrp expressors (M-V+) and wild type (M+V+) exhibited higher average bacterial CFU per IJ than did high-Lrp (M+V-) or no-Lrp (M-V-) strains. Further, the bacterial population becomes increasingly low-Lrp expressing, based on expression of an Lrp-dependent fluorescent reporter, as IJs age. These data support a model that virulent X. nematophila have a selective advantage and accumulate in aging IJs in advance of exposure to insect hosts in which this phenotype is necessary.
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Affiliation(s)
- Mengyi Cao
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Heidi Goodrich-Blair
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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41
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Hochstetter A, Vernekar R, Austin RH, Becker H, Beech JP, Fedosov DA, Gompper G, Kim SC, Smith JT, Stolovitzky G, Tegenfeldt JO, Wunsch BH, Zeming KK, Krüger T, Inglis DW. Deterministic Lateral Displacement: Challenges and Perspectives. ACS NANO 2020; 14:10784-10795. [PMID: 32844655 DOI: 10.1021/acsnano.0c05186] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The advent of microfluidics in the 1990s promised a revolution in multiple industries from healthcare to chemical processing. Deterministic lateral displacement (DLD) is a continuous-flow microfluidic particle separation method discovered in 2004 that has been applied successfully and widely to the separation of blood cells, yeast, spores, bacteria, viruses, DNA, droplets, and more. Deterministic lateral displacement is conceptually simple and can deliver consistent performance over a wide range of flow rates and particle concentrations. Despite wide use and in-depth study, DLD has not yet been fully elucidated or optimized, with different approaches to the same problem yielding varying results. We endeavor here to provide up-to-date expert opinion on the state-of-art and current fundamental, practical, and commercial challenges with DLD as well as describe experimental and modeling opportunities. Because these challenges and opportunities arise from constraints on hydrodynamics, fabrication, and operation at the micro- and nanoscale, we expect this Perspective to serve as a guide for the broader micro- and nanofluidic community to identify and to address open questions in the field.
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Affiliation(s)
- Axel Hochstetter
- Department of Physics, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Rohan Vernekar
- School of Engineering, Institute for Multiscale Thermofluids, University of Edinburgh, EH9 3DW Edinburgh, United Kingdom
| | - Robert H Austin
- Department of Physics, Princeton University, Princeton 08544, New Jersey, United States
| | | | - Jason P Beech
- Department of Physics and NanoLund, Lund University, SE 22100 Lund, Sweden
| | - Dmitry A Fedosov
- Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Juelich, Germany
| | - Gerhard Gompper
- Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Juelich, Germany
| | - Sung-Cheol Kim
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Joshua T Smith
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Gustavo Stolovitzky
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jonas O Tegenfeldt
- Department of Physics and NanoLund, Lund University, SE 22100 Lund, Sweden
| | - Benjamin H Wunsch
- IBM T.J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Kerwin K Zeming
- Critical Analytics for Manufacturing of Personalized Medicine, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Timm Krüger
- School of Engineering, Institute for Multiscale Thermofluids, University of Edinburgh, EH9 3DW Edinburgh, United Kingdom
| | - David W Inglis
- School of Engineering, Macquarie University, Macquarie Park, New South Wales 2109, Australia
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Javadi A, Arrieta J, Tuval I, Polin M. Photo-bioconvection: towards light control of flows in active suspensions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190523. [PMID: 32762429 PMCID: PMC7422871 DOI: 10.1098/rsta.2019.0523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The persistent motility of individual constituents in microbial suspensions represents a prime example of the so-called active matter systems. Cells consume energy, exert forces and move, overall releasing the constraints of equilibrium statistical mechanics of passive elements and allowing for complex spatio-temporal patterns to emerge. Moreover, when subject to physico-chemical stimuli their collective behaviour often drives large-scale instabilities of a hydrodynamic nature, with implications for biomixing in natural environments and incipient industrial applications. In turn, our ability to exert external control of these driving stimuli could be used to govern the emerging patterns. Light, being easily manipulable and, at the same time, an important stimulus for a wide variety of microorganisms, is particularly well suited to this end. In this paper, we will discuss the current state, developments and some of the emerging advances in the fundamentals and applications of light-induced bioconvection with a focus on recent experimental realizations and modelling efforts. This article is part of the theme issue 'Stokes at 200 (part 2)'.
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Affiliation(s)
- A. Javadi
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- e-mail:
| | - J. Arrieta
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, 07190 Esporles, Spain
| | - I. Tuval
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, 07190 Esporles, Spain
- Departamento de Física, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
| | - M. Polin
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- Centre for Mechanochemical Cell Biology, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- e-mail:
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43
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Tang Q, Yang X, Xuan C, Wu K, Lai C, Shi X. Generation of microfluidic gradients and their effects on cells behaviours. Biodes Manuf 2020. [DOI: 10.1007/s42242-020-00093-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Cama J, Voliotis M, Metz J, Smith A, Iannucci J, Keyser UF, Tsaneva-Atanasova K, Pagliara S. Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. LAB ON A CHIP 2020; 20:2765-2775. [PMID: 32613221 PMCID: PMC7953842 DOI: 10.1039/d0lc00242a] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/15/2020] [Indexed: 06/01/2023]
Abstract
The double-membrane cell envelope of Gram-negative bacteria is a formidable barrier to intracellular antibiotic accumulation. A quantitative understanding of antibiotic transport in these cells is crucial for drug development, but this has proved elusive due to a dearth of suitable investigative techniques. Here we combine microfluidics and time-lapse auto-fluorescence microscopy to rapidly quantify antibiotic accumulation in hundreds of individual Escherichia coli cells. By serially manipulating the microfluidic environment, we demonstrated that stationary phase Escherichia coli, traditionally more refractory to antibiotics than growing cells, display reduced accumulation of the antibiotic ofloxacin compared to actively growing cells. Our novel microfluidic method facilitates the quantitative comparison of the role of the microenvironment versus that of the absence of key membrane transport pathways in cellular drug accumulation. Unlike traditional techniques, our assay is rapid, studying accumulation as the cells are dosed with the drug. This platform provides a powerful new tool for studying antibiotic accumulation in bacteria, which will be critical for the rational development of the next generation of antibiotics.
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Affiliation(s)
- Jehangir Cama
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Margaritis Voliotis
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Jeremy Metz
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ashley Smith
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Jari Iannucci
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
| | - Ulrich F. Keyser
- Cavendish Laboratory
, Department of Physics
, University of Cambridge
,
JJ Thomson Avenue
, Cambridge CB3 0HE
, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- College of Engineering
, Mathematics and Physical Sciences
, University of Exeter
,
Exeter EX4 4QF
, UK
| | - Stefano Pagliara
- Living Systems Institute
, University of Exeter
,
Exeter EX4 4QD
, UK
.
- School of Biosciences
, College of Life and Environmental Sciences
, University of Exeter
,
Exeter EX4 4QD
, UK
.
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45
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Grigolato F, Egholm C, Impellizzieri D, Arosio P, Boyman O. Establishment of a scalable microfluidic assay for characterization of population-based neutrophil chemotaxis. Allergy 2020; 75:1382-1393. [PMID: 31971608 DOI: 10.1111/all.14195] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Regulation of neutrophil chemotaxis and activation plays crucial roles in immunity, and dysregulated neutrophil responses can lead to pathology as seen in neutrophilic asthma. Neutrophil recruitment is key for initiating immune defense and inflammation, and its modulation is a promising therapeutic target. Microfluidic technology is an attractive tool for characterization of neutrophil migration. Compared to transwell assays, microfluidic approaches could offer several advantages, including precis e control of defined chemokine gradients in space and time, automated quantitative analysis of chemotaxis, and high throughput. METHODS We established a microfluidic device for fully automated, quantitative assessment of neutrophil chemotaxis. Freshly isolated mouse neutrophils from bone marrow or human neutrophils from peripheral blood were assessed in real time using an epifluorescence microscope for their migration toward the potent chemoattractants C-X-C-motif ligand 2 (CXCL2) and CXCL8, without or with interleukin-4 (IL-4) pre-incubation. RESULTS Our microfluidic device allowed the precise and reproducible determination of the optimal CXCL2 and CXCL8 concentrations for mouse and human neutrophil chemotaxis, respectively. Furthermore, our microfluidic assay was able to measure the equilibrium and real-time dynamic effects of specific modulators of neutrophil chemotaxis. We demonstrated this concept by showing that IL-4 receptor signaling in mouse and human neutrophils inhibited their migration toward CXCL2 and CXCL8, respectively, and this inhibition was time-dependent. CONCLUSION Collectively, our microfluidic device shows several advantages over traditional transwell migration assays and its design is amenable to future integration into multiplexed high-throughput platforms for screening of molecules that modulate the chemotaxis of different immune cells.
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Affiliation(s)
- Fulvio Grigolato
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology, Zurich Zurich Switzerland
| | - Cecilie Egholm
- Department of Immunology University Hospital Zurich Zurich Switzerland
| | | | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology, Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
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46
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Berendsen JTW, Kruit SA, Atak N, Willink E, Segerink LI. Flow-Free Microfluidic Device for Quantifying Chemotaxis in Spermatozoa. Anal Chem 2020; 92:3302-3306. [PMID: 31994387 PMCID: PMC7031847 DOI: 10.1021/acs.analchem.9b05183] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Current male fertility diagnosis tests focus on assessing the quality of semen samples by studying the concentration, total volume, and motility of spermatozoa. However, other characteristics such as the chemotactic ability of a spermatozoon might influence the chance of fertilization. Here we describe a simple, easy to fabricate and handle, flow-free microfluidic chip to test the chemotactic response of spermatozoa made out of a hybrid hydrogel (8% gelatin/1% agarose). A chemotaxis experiment with 1 μM progesterone was performed that significantly demonstrated that boar spermatozoa are attracted by a progesterone gradient.
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Affiliation(s)
- Johanna T W Berendsen
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , 7500 AE Enschede , The Netherlands
| | - Stella A Kruit
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , 7500 AE Enschede , The Netherlands
| | - Nihan Atak
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , 7500 AE Enschede , The Netherlands
| | - Ellen Willink
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , 7500 AE Enschede , The Netherlands
| | - Loes I Segerink
- BIOS-Lab on a Chip Group, MESA+ Institute for Nanotechnology and MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , 7500 AE Enschede , The Netherlands
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47
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Gurung JP, Gel M, Baker MAB. Microfluidic techniques for separation of bacterial cells via taxis. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 7:66-79. [PMID: 32161767 PMCID: PMC7052948 DOI: 10.15698/mic2020.03.710] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/24/2019] [Accepted: 01/10/2020] [Indexed: 12/22/2022]
Abstract
The microbial environment is typically within a fluid and the key processes happen at the microscopic scale where viscosity dominates over inertial forces. Microfluidic tools are thus well suited to study microbial motility because they offer precise control of spatial structures and are ideal for the generation of laminar fluid flows with low Reynolds numbers at microbial lengthscales. These tools have been used in combination with microscopy platforms to visualise and study various microbial taxes. These include establishing concentration and temperature gradients to influence motility via chemotaxis and thermotaxis, or controlling the surrounding microenvironment to influence rheotaxis, magnetotaxis, and phototaxis. Improvements in microfluidic technology have allowed fine separation of cells based on subtle differences in motility traits and have applications in synthetic biology, directed evolution, and applied medical microbiology.
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Affiliation(s)
- Jyoti P. Gurung
- School of Biotechnology and Biomolecular Science, UNSW Sydney
| | - Murat Gel
- CSIRO Manufacturing, Clayton
- CSIRO Future Science Platform for Synthetic Biology
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science, UNSW Sydney
- CSIRO Future Science Platform for Synthetic Biology
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48
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Tong W, Yao X, Duan S, Yu B, Ding X, Ding X, Xu FJ. Gradient Functionalization of Various Quaternized Polyethylenimines on Microfluidic Chips for the Rapid Appraisal of Antibacterial Potencies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:354-361. [PMID: 31826611 DOI: 10.1021/acs.langmuir.9b02747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability to appraise antibacterial potencies of surface-immobilized bactericidal polymers is still a major challenge in the engineering of antibacterial surfaces to combat hospital-acquired (nosocomial) infections. In this work, we fabricated a microfluidic platform with gradiently immobilized bactericidal polymers to enable the rapid appraisal of antibacterial potencies by in situ live/dead staining of bacteria. To this end, a variety of synthetic quaternary polymers, named QPEI-C1, QPEI-C6, QPEI-C8, and QPEI-C10, were gradiently immobilized in microfluidic channels, and their surface densities at different distances along the channels were quantified by using fluorescein-labeled polymers. We found that the surface densities of quaternary polymers could be well-tuned, and the length of the channel, resulting in a 50% reduction of live bacteria (L50), can be used to appraise the antibacterial potency of each bactericidal polymer. For instance, the L50 values of QPEI-C6-, QPEI-C8-, and QPEI-C10-modified channels against Escherichia coli were 35.5, 44.7, and 49.2 mm, respectively, indicating that QPEI-C10 exerted the most potent antibacterial efficacy. More importantly, this microfluidic platform enabled the rapid discrimination of antibacterial potencies of polymers (e.g., QPEI-C8, and QPEI-C10) while the conventional live/dead staining method found no significant difference. This work provides a powerful toolkit by combining advances of microfluidic systems and polymer science for the rapid screening of antibacterial coatings, which would find applications in surface modification of medical devices to combat bacterial infections.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xin Yao
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Shun Duan
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Bingran Yu
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xiaokang Ding
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Xuejia Ding
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Fu-Jian Xu
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing Advanced Innovation Center for Soft Matter Science and Engineering and Key Lab of Biomedical Materials of Natural Macromolecules, Ministry of Education , Beijing University of Chemical Technology , Beijing 100029 , China
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Abstract
Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found. Synthetic biology uses cells as its computing substrate, often based on the genetic circuit concept. In this Perspective, the authors argue that existing synthetic biology approaches based on classical models of computation limit the potential of biocomputing, and propose that living organisms have under-exploited capabilities.
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50
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Gasperotti A, Brameyer S, Fabiani F, Jung K. Phenotypic heterogeneity of microbial populations under nutrient limitation. Curr Opin Biotechnol 2019; 62:160-167. [PMID: 31698311 DOI: 10.1016/j.copbio.2019.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Phenotypic heterogeneity is a phenomenon in which genetically identical individuals have different characteristics. This behavior can also be found in bacteria, even if they grow as monospecies in well-mixed environments such as bioreactors. Here it is discussed how phenotypic heterogeneity is generated by internal factors and how it is promoted under nutrient-limited growth conditions. A better understanding of the molecular levels that control phenotypic heterogeneity could improve biotechnological production processes.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Florian Fabiani
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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